topaz.convert module

class topaz.convert.CsvCoordinateList(filename, mode='r', score=False)

Bases: topaz.convert.CsvImageList

Handler class to write a list of particles as expected by topaz.

addCoord(micId, x, y)

class topaz.convert.CsvImageList(filename, mode='r', **kwargs)

Bases: object

Handler class to write a list of images as expected by topaz.

close()

class topaz.convert.CsvMicrographList(filename, mode='r')

Bases: topaz.convert.CsvImageList

Handler class to write a list of micrographs as expected by topaz.

addMic(micId, micPath)

topaz.convert.convertMicrographs(micList, micDir)

Convert (or simply link) input micrographs into the given directory in a format that is compatible with Topaz.

topaz.convert.getMicIdName(mic, suffix='')

Return a name for the micrograph based on its IDs.

topaz.convert.readSetOfCoordinates(coordinatesCsvFn, micSet, coordSet, scale)

Read coordinates produced by Topaz. Coordinates are expected in a single csv file, with the following columns:

first: image_name (mic id) second: x_coord third: y_coord forth: score